Three years have passed since the Cerise Island incident in Kanto. Enter Gold from the neighbouring Johto, a happy-go-lucky boy whose mischief earns him more troubles than merits. Setting out on a journey to chase down Silver, a mysterious thief boy who stole Totodile from Prof Elm's lab, Gold got the chance to meet Gymleaders and other prominent figures in the region. However, he soon found himself intertwined in the evil schemes of the resurrected Team Rocket, now under the leadership of the ominous masked man.

Meanwhile, Crystal, a young capture specialist, was hired by Professor Oak to help complete his neglected Pokedex. After an encounter with the powerful legendary Pokemon, Suicune, the girl became determined to catch it, but little did she know that Suicune was actually in search of a trusted partner who could help it thwart an evil looming on the horizon, an evil whose work began 9 years ago, and could potentially bring havoc to both Kanto and Johto...